Arunachalam, P. S. et al. Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science 369, 12101220 (2020).
Article ADS CAS PubMed PubMed Central Google Scholar
Shen-Orr, S. S. & Furman, D. Variability in the immune system: of vaccine responses and immune states. Curr. Opin. Immunol. 25, 542547 (2013).
Article CAS PubMed PubMed Central Google Scholar
Yofe, I., Dahan, R. & Amit, I. Single-cell genomic approaches for developing the next generation of immunotherapies. Nat. Med. 26, 171177 (2020).
Article CAS PubMed Google Scholar
Banchereau, R., Cepika, A.-M. & Pascual, V. Systems approaches to human autoimmune diseases. Curr. Opin. Immunol. 25, 598605 (2013).
Article CAS PubMed PubMed Central Google Scholar
Davis, M. M., Tato, C. M. & Furman, D. Systems immunology: just getting started. Nat. Immunol. 18, 725732 (2017).
Article CAS PubMed PubMed Central Google Scholar
Germain, R. N., Meier-Schellersheim, M., Nita-Lazar, A. & Fraser, I. D. C. Systems biology in immunology: a computational modeling perspective. Annu. Rev. Immunol. 29, 527585 (2011).
Article CAS PubMed PubMed Central Google Scholar
Ma, S. et al. Chromatin potential identified by shared single-cell profiling of RNA and chromatin. Cell 183, 11031116 (2020). This work pioneered paired sequencing of chromatin accessibility and transcriptome in single cells (SHARE-seq).
Article CAS PubMed PubMed Central Google Scholar
Sthl, P. L. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 7882 (2016). This work pioneered spatially resolved transcriptomics.
Article ADS PubMed Google Scholar
Regev, A. et al. The Human Cell Atlas. eLife https://doi.org/10.7554/eLife.27041 (2017).
Domnguez Conde, C. et al. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science 376, eabl5197 (2022).
Article PubMed PubMed Central Google Scholar
HuBMAP Consortium. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature 574, 187192 (2019).
Article ADS CAS Google Scholar
Martin, F. J. et al. Ensembl 2023. Nucleic Acids Res. 51, D933D941 (2023).
Article CAS PubMed Google Scholar
UniProt Consortium. Uniprot: the universal protein knowledgebase in 2023. Nucleic Acids Res. 51, D523D531 (2023).
Article Google Scholar
Trei, D. et al. Integrated intra and intercellular signaling knowledge for multicellular omics analysis. Mol. Syst. Biol. 17, e9923 (2021). This work introduces a comprehensive meta-resource that collects data from over a hundred databases, including, for example, protein interaction networks, ligandreceptor annotations and protein complex information.
Article PubMed PubMed Central Google Scholar
Szklarczyk, D. et al. STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. Nucleic Acids Res. 44, D380D384 (2016).
Article CAS PubMed Google Scholar
Garcia-Alonso, L., Holland, C. H., Ibrahim, M. M., Turei, D. & Saez-Rodriguez, J. Benchmark and integration of resources for the estimation of human transcription factor activities. Genome Res. 29, 13631375 (2019).
Article CAS PubMed PubMed Central Google Scholar
Schubert, M. et al. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nat. Commun. 9, 20 (2018).
Article ADS PubMed PubMed Central Google Scholar
Armingol, E., Officer, A., Harismendy, O. & Lewis, N. E. Deciphering cell-cell interactions and communication from gene expression. Nat. Rev. Genet. 22, 7188 (2021).
Article CAS PubMed Google Scholar
Vandereyken, K., Sifrim, A., Thienpont, B. & Voet, T. Methods and applications for single-cell and spatial multi-omics. Nat. Rev. Genet. 24, 494515 (2023).
Article CAS PubMed Google Scholar
Baysoy, A., Bai, Z., Satija, R. & Fan, R. The technological landscape and applications of single-cell multi-omics. Nat. Rev. Mol. Cell Biol. 24, 695713 (2023).
Article CAS PubMed Google Scholar
Bonaguro, L. et al. A guide to systems-level immunomics. Nat. Immunol. 23, 14121423 (2022).
Article CAS PubMed Google Scholar
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 18881902 (2019).
Article CAS PubMed PubMed Central Google Scholar
Heumos, L. et al. Best practices for single-cell analysis across modalities. Nat. Rev. Genet. 24, 550572 (2023).
Article CAS PubMed Google Scholar
Amezquita, R. A. et al. Orchestrating single-cell analysis with Bioconductor. Nat. Methods 17, 137145 (2020).
Article CAS PubMed Google Scholar
Gene Ontology Consortium et al. The Gene Ontology knowledgebase in 2023. Genetics 224, iyad031 (2023).
Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M. & Ishiguro-Watanabe, M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 51, D587D592 (2023).
Article CAS PubMed Google Scholar
Gillespie, M. et al. The reactome pathway knowledgebase 2022. Nucleic Acids Res. 50, D687D692 (2022).
Article CAS PubMed Google Scholar
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 1554515550 (2005).
Article ADS CAS PubMed PubMed Central Google Scholar
Vremo, L., Nielsen, J. & Nookaew, I. Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods. Nucleic Acids Res. 41, 43784391 (2013).
Article PubMed PubMed Central Google Scholar
Badia-I-Mompel, P. et al. decoupleR: ensemble of computational methods to infer biological activities from omics data. Bioinform. Adv. 2, vbac016 (2022).
Article PubMed PubMed Central Google Scholar
Hosokawa, H. & Rothenberg, E. V. How transcription factors drive choice of the T cell fate. Nat. Rev. Immunol. 21, 162176 (2021).
Article CAS PubMed Google Scholar
Kawasaki, T. & Kawai, T. Toll-like receptor signaling pathways. Front. Immunol. 5, 461 (2014).
Article PubMed PubMed Central Google Scholar
Saini, A., Ghoneim, H. E., Lio, C. -W. J., Collins, P. L. & Oltz, E. M. Gene regulatory circuits in innate and adaptive immune cells. Annu. Rev. Immunol. 40, 387411 (2022).
Article CAS PubMed PubMed Central Google Scholar
Liu, Z.-P., Wu, C., Miao, H. & Wu, H. RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. Database 2015, bav095 (2015).
Article PubMed PubMed Central Google Scholar
Keenan, A. B. et al. ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res. 47, W212W224 (2019).
Article CAS PubMed PubMed Central Google Scholar
Mller-Dott, S. et al. Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities. Nucleic Acids Res. 51, 1093410949 (2023).
Article PubMed PubMed Central Google Scholar
Holland, C. H. et al. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Genome Biol. 21, 36 (2020).
Article CAS PubMed PubMed Central Google Scholar
Zeitlinger, J. Seven myths of how transcription factors read the cis-regulatory code. Curr. Opin. Syst. Biol. 23, 2231 (2020).
Article PubMed PubMed Central Google Scholar
Fiers, M. W. E. J. et al. Mapping gene regulatory networks from single-cell omics data. Brief. Funct. Genomics 17, 246254 (2018).
Article CAS PubMed PubMed Central Google Scholar
Chen, S. & Mar, J. C. Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data. BMC Bioinformatics 19, 232 (2018).
Article PubMed PubMed Central Google Scholar
Pratapa, A., Jalihal, A. P., Law, J. N., Bharadwaj, A. & Murali, T. M. Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data. Nat. Methods 17, 147154 (2020).
Article CAS PubMed PubMed Central Google Scholar
Badia-I-Mompel, P. et al. Gene regulatory network inference in the era of single-cell multi-omics. Nat. Rev. Genet. 24, 739754 (2023).
Article CAS PubMed Google Scholar
Wayman, J. A. et al. An atlas of gene regulatory networks for memory CD4+ T cells in youth and old age. Preprint at BioRxiv https://doi.org/10.1101/2023.03.07.531590 (2023).
Chowdhary, K. & Benoist, C. A variegated model of transcription factor function in the immune system. Trends Immunol. 44, 530541 (2023).
Article CAS PubMed Google Scholar
Bravo Gonzlez-Blas, C. et al. SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. Nat. Methods 20, 13551367 (2023).
Article PubMed PubMed Central Google Scholar
Kramer, B. A., Sarabia Del Castillo, J. & Pelkmans, L. Multimodal perception links cellular state to decision-making in single cells. Science 377, 642648 (2022).
Article ADS CAS PubMed Google Scholar
Weidemller, P., Kholmatov, M., Petsalaki, E. & Zaugg, J. B. Transcription factors: bridge between cell signaling and gene regulation. Proteomics 21, e2000034 (2021).
Article PubMed Google Scholar
Deribe, Y. L., Pawson, T. & Dikic, I. Post-translational modifications in signal integration. Nat. Struct. Mol. Biol. 17, 666672 (2010).
Article CAS PubMed Google Scholar
Lun, X. -K. & Bodenmiller, B. Profiling cell signaling networks at single-cell resolution. Mol. Cell. Proteom. 19, 744756 (2020).
Article CAS Google Scholar
Dugourd, A. & Saez-Rodriguez, J. Footprint-based functional analysis of multiomic data. Curr. Opin. Syst. Biol. 15, 8290 (2019).
Article PubMed PubMed Central Google Scholar
Rydenfelt, M., Klinger, B., Klnemann, M. & Blthgen, N. SPEED2: inferring upstream pathway activity from differential gene expression. Nucleic Acids Res. 48, W307W312 (2020).
Article CAS PubMed PubMed Central Google Scholar
Jiang, P. et al. Systematic investigation of cytokine signaling activity at the tissue and single-cell levels. Nat. Methods 18, 11811191 (2021). This work introduced a comprehensive resource describing how cytokines affect gene expression, which can be used to infer cytokine activity from transcriptomics data.
See original here:
Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system - Nature.com
- Fellow Focus in Four: Marat Kribis, MD, Rheumatology, Allergy and Immunology - Yale School of Medicine - April 15th, 2024 [April 15th, 2024]
- Long COVID Can Now Be Detected in the Blood - Technology Networks - April 15th, 2024 [April 15th, 2024]
- Rimjhim Agarwal selected as Major Symposium speaker at the American Association of Immunologists ... - La Jolla Institute for Immunology - March 29th, 2024 [March 29th, 2024]
- Seeking new horizons: Where innovators find opportunities in a fast-changing immunology landscape - IQVIA - March 29th, 2024 [March 29th, 2024]
- Researchers identify new way to inhibit immune cells that drive allergic asthma - EurekAlert - March 29th, 2024 [March 29th, 2024]
- Innovation in Oncology and Cancer Immunology Research - Boehringer Ingelheim - March 29th, 2024 [March 29th, 2024]
- Measles outbreaks show the risk of under-vaccination | News | Harvard T.H. Chan School of Public Health - HSPH News - March 29th, 2024 [March 29th, 2024]
- Immunology-oncology ELISA Kits Market to Witness a Healthy Growth by 2030 - WhaTech - March 29th, 2024 [March 29th, 2024]
- Spring Allergy Season Is Getting Worse. Here's What to Know. - The New York Times - March 29th, 2024 [March 29th, 2024]
- Multiple sclerosis has distinct subtypes, study finds, pointing to different treatments - STAT - March 29th, 2024 [March 29th, 2024]
- Researchers identify viable vaccine targets for hepatitis C infections - News-Medical.Net - March 29th, 2024 [March 29th, 2024]
- Three research projects awarded funding from the Immunology Institute Pilot Project program - University of Alabama at Birmingham - February 29th, 2024 [February 29th, 2024]
- Deal Watch: AbbVie Adds To Immunology Pipeline Through Deal With OSE - Scrip - February 29th, 2024 [February 29th, 2024]
- AbbVie and Tentarix Announce Collaboration to Develop Conditionally-Active, Multi-Specific Biologics for Oncology ... - PR Newswire - February 29th, 2024 [February 29th, 2024]
- Renowned immunologist and four-decade UAB researcher Max Cooper, M.D., will deliver this year's Marx Lecture - University of Alabama at Birmingham - February 29th, 2024 [February 29th, 2024]
- Inactivation of TGF- signaling in CAR-T cells | Cellular & Molecular Immunology - Nature.com - February 29th, 2024 [February 29th, 2024]
- Babies use their immune system differently but efficiently | Cornell Chronicle - Cornell Chronicle - February 29th, 2024 [February 29th, 2024]
- Antibody reduces allergic reactions to multiple foods in NIH clinical trial - National Institutes of Health (NIH) (.gov) - February 29th, 2024 [February 29th, 2024]
- Mestag Therapeutics Enlists Leading Cancer Biology and Immunology Advisors to Support Clinical Development of its ... - GlobeNewswire - February 21st, 2024 [February 21st, 2024]
- Theratechnologies announces publication in Frontiers in Immunology on TH1902 - TipRanks.com - TipRanks - February 21st, 2024 [February 21st, 2024]
- Smoking has long-term effects on the immune system - Institut Pasteur - February 21st, 2024 [February 21st, 2024]
- Spring Allergies Attack More Than Just Your Nose - ACAAI Public Website - American College of Allergy Asthma and Immunology - February 21st, 2024 [February 21st, 2024]
- Theratechnologies Announces Publication in Frontiers in Immunology that Deepens Understanding of Sudocetaxel ... - GlobeNewswire - February 21st, 2024 [February 21st, 2024]
- Shikhar Mehrotra named co-leader of Cancer Biology and Immunology research program at MUSC Hollings - The Cancer Letter - January 27th, 2024 [January 27th, 2024]
- Gut Microbiome Benefits of Breast Milk Revealed in Mouse Study - Technology Networks - January 27th, 2024 [January 27th, 2024]
- Research on Immunological Diseases Launches with Hungarian Participation - Hungary Today - January 27th, 2024 [January 27th, 2024]
- UCLA to turn former shopping mall into centers for research on immunology and quantum science - The Associated Press - January 8th, 2024 [January 8th, 2024]
- TRexBio Announces a First Option Was Exercised by Partner under Immunology Discovery Collaboration - Business Wire - January 8th, 2024 [January 8th, 2024]
- UCLA to turn former Westside Pavilion into centers for research on immunology and quantum science - KABC-TV - January 8th, 2024 [January 8th, 2024]
- HI-Bio Announces $95 Million Series B Financing to Advance Targeted Therapies for Immune-Mediated Diseases - PR Newswire - January 8th, 2024 [January 8th, 2024]
- Beyond Cytotoxicity: The Importance of T Cell Memory - The Scientist - January 8th, 2024 [January 8th, 2024]
- IKAROS: Unlocking the secrets of the immune system's key player - News-Medical.Net - January 8th, 2024 [January 8th, 2024]
- UCLA to turn former shopping mall into centers for research on immunology and quantum science - The Caledonian-Record - January 8th, 2024 [January 8th, 2024]
- Revolutionizing Vaccine Research: The Power of a New Algorithm - SciTechDaily - December 31st, 2023 [December 31st, 2023]
- Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people ... - Nature.com - December 22nd, 2023 [December 22nd, 2023]
- Two new practice parameters offer recommendations for treating anaphylaxis and atopic dermatitis - News-Medical.Net - December 22nd, 2023 [December 22nd, 2023]
- Physician and Patient (Un)Wellness in Allergy and Immunology During COVID-19 and Beyond: Lessons for the Future - Physician's Weekly - December 22nd, 2023 [December 22nd, 2023]
- Researchers Identify Why Some Cancers Do Not Respond to Immunotherapy - NYU Langone Health - December 22nd, 2023 [December 22nd, 2023]
- MU's Haval Shirwan recognized for achievements in immunology - Columbia Daily Tribune - December 22nd, 2023 [December 22nd, 2023]
- Parker Institute for Cancer Immunotherapy (PICI) Welcomes Weill Cornell Medicine to Cancer Research Consortium - Weill Cornell Medicine Newsroom - December 14th, 2023 [December 14th, 2023]
- Annals of Allergy, Asthma and Immunology Examines Effects of Climate Change on Allergic Conditions - Newswise - December 14th, 2023 [December 14th, 2023]
- British Society for Immunology response to the NHS vaccination strategy - British Society for Immunology | - December 14th, 2023 [December 14th, 2023]
- NYU Langone Health in the NewsFriday, December 8, 2023 - NYU Langone Health - December 14th, 2023 [December 14th, 2023]
- Arturo Casadevall Named Distinguished Fellow by the American Association of Immunologists - Johns Hopkins Bloomberg School of Public Health - December 14th, 2023 [December 14th, 2023]
- ImmunoScape Appoints Systems Immunology and Computational Biology Expert Dr. John Tsang to its Scien - PharmiWeb.com - December 14th, 2023 [December 14th, 2023]
- Ishares Genomics Immunology And Healthcare Etf ($IDNA) Proactive Strategies - Stock Traders Daily - December 14th, 2023 [December 14th, 2023]
- Medical Breakthroughs Fueling Infection Prevention Market: Immunology and Modern Medicine Advancements to ... - PR Newswire - December 14th, 2023 [December 14th, 2023]
- Cancer therapy bexmarilimab awakens immune cells to attack tumors that have avoided the detection of the immune ... - EurekAlert - December 14th, 2023 [December 14th, 2023]
- Testing Cancer Immunotherapies on Mice with Human Immune Systems - Mirage News - December 14th, 2023 [December 14th, 2023]
- Georgetown School of Medicine's Department of Immunology Hosts Talk About Therapeutic Vaccine for Autoimmune ... - Georgetown University The Hoya - December 6th, 2023 [December 6th, 2023]
- Long COVID Research Is a Bit of a Mess - Technology Networks - December 6th, 2023 [December 6th, 2023]
- Research Assistant/Research Associate in Immunology job with ... - Times Higher Education - May 13th, 2023 [May 13th, 2023]
- Pioneering learning resource helps academic win top teaching award - Swansea University - May 13th, 2023 [May 13th, 2023]
- 12 Months of Treatment with EPIT Superior to Placebo in ... - UNC Health and UNC School of Medicine - May 13th, 2023 [May 13th, 2023]
- Director of Discover Biology, Neuroscience & Immunology- full-time ... - Merck KGaA - May 13th, 2023 [May 13th, 2023]
- Absci, The Kennedy Institute for immunotherapies development - Pharmaceutical Technology - May 13th, 2023 [May 13th, 2023]
- Customizing T Cell-Based Immunotherapies in a 'SNAP' - UPMC - May 13th, 2023 [May 13th, 2023]
- Understanding Lupus: an interview with the Garvan Institute - News-Medical.Net - May 13th, 2023 [May 13th, 2023]
- Professor Laura Mackay wins LEO Foundation Award in Region ... - The Peter Doherty Institute for Infection and Immunity - May 13th, 2023 [May 13th, 2023]
- Trinity's Prof Ed Lavelle recognised by ISI for vaccine research - SiliconRepublic.com - May 13th, 2023 [May 13th, 2023]
- Allison Institute announces appointment of inaugural members - EurekAlert - May 13th, 2023 [May 13th, 2023]
- Study sheds light on how the immune system protects the body - EurekAlert - May 13th, 2023 [May 13th, 2023]
- Werewolf Therapeutics Reports First Quarter 2023 Financial Results ... - BioSpace - May 13th, 2023 [May 13th, 2023]
- PeaceHealth cuts Bellingham jobs, announces clinic closure and reduces some services - Yahoo News - May 13th, 2023 [May 13th, 2023]
- Help! My skin is itchy - Parkview Health - May 13th, 2023 [May 13th, 2023]
- Takeda reports 12.8% rise in FY2022 revenue - Pharmaceutical Technology - May 13th, 2023 [May 13th, 2023]
- Welcoming a new column: Vasso's corner - The immune system - Neos Kosmos - May 13th, 2023 [May 13th, 2023]
- UC statement on Gov. Newsom's 2023-24 revised budget proposal - University of California - May 13th, 2023 [May 13th, 2023]
- Jasper Therapeutics (JSPR) Appoints Stephen J. Galli to its Board - StreetInsider.com - May 13th, 2023 [May 13th, 2023]
- DICE Therapeutics Reports First Quarter 2023 Financial Results and ... - InvestorsObserver - May 13th, 2023 [May 13th, 2023]
- Cannabis-derived products have flooded US market Two ... - Down To Earth Magazine - May 13th, 2023 [May 13th, 2023]
- NYU Langone Health in the NewsFriday, May 12, 2023 - NYU Langone Health - May 13th, 2023 [May 13th, 2023]
- UNION therapeutics to present at 4th Annual Dermatology Drug ... - InvestorsObserver - May 13th, 2023 [May 13th, 2023]
- Russell Investments Decreases Stake in Argenx SE by 20% in Q4 ... - Best Stocks - May 13th, 2023 [May 13th, 2023]
- How my training helps me to address health disparities in multiple ... - Nature.com - May 13th, 2023 [May 13th, 2023]
- Positive trial results for RSV infant treatment: Sanofi - Medical Xpress - May 13th, 2023 [May 13th, 2023]
- How Can You Find Out If You're Allergic to a Medication Before You ... - Verywell Health - May 13th, 2023 [May 13th, 2023]
- HUTCHMED Announces Appointment of Independent Non ... - GlobeNewswire - May 13th, 2023 [May 13th, 2023]
- The Wistar Institute, Pennsylvania Biotechnology Center and Baruch S. Blumberg Institute Forge Strategic Collaboration to Support Regional Biotech... - May 13th, 2023 [May 13th, 2023]
- Humanized Mouse and Rat Model Market worth $338 million | MarketsandMarkets - Yahoo Finance - May 13th, 2023 [May 13th, 2023]